Publications
Scientific papers
2025
- Improving drug repositioning with negative data labeling using large language models
M. Picard, M. Leclercq, A. Bodein, M.P. Scott-Boyer, O. Perin, A. Droit
Journal of Cheminformatics, https://doi.org/10.1186/s13321-025-00962-0
2024
Target repositioning using multi-layer networks and machine learning: the case of prostate cancer
M. Picard, M.P. Scott-Boyer, A. Bodein, M. Leclercq, J. Prunier, O. Perin, A. Droit
Computational and Structural Biotechnology Journal, https://doi.org/10.1016/j.csbj.2024.06.012Combined transcriptomics and proteomics unveil the impact of vitamin C in modulating specific protein abundance in the mouse liver
Aumailley, L., Bodein A., Adjibade, P. et al.
BMC Biological Research, https://doi.org/10.1186/s40659-024-00509-xProteomic Profiling of Samples Derived from a Murine Model Following Cryptococcus neoformans Infection
Muselius B., A. Bodein, Roux-Dalvai F., Droit A., Geddes-McAlister J.
Methods in Molecular Biology (Book chapter), https://doi.org/10.1007/978-1-0716-3722-7_9SOS genes are rapidly induced while translesion synthesis polymerase activity is temporally regulated
O. E. T. Bergum, A. H. Singleton, L. M. Røst, A. Bodein, M.-P. Scott-Boyer, M. B. Rye, A. Droit, P. Bruheim, M. Otterlei
Frontiers in Microbiology, https://doi.org/10.3389/fmicb.2024.1373344
2023
Multi-Omics Data Integration Reveals Key Variables Contributing to Subgingival Microbiome Dysbiosis-Induced Inflammatory Response in a Hyperglycemic Microenvironment
S. Lafleur\(^\star\), A. Bodein\(^\star\), J. M. M. Mutombo, A. Mathieu, C. Joly Beauparlant, X. Minne, F. Chandad, A. Droit, V. P. Houde
International Journal of Molecular Sciences, https://doi.org/10.3390/ijms24108832High dairy products intake modifies the correlation between α-tocopherol levels and serum proteins related to lipid metabolism in subjects at risk of type 2 diabetes
A. Mahdavi, M. Leclercq, A. Bodein, C. Gotti, K. Greffard, J.F. Bilodeau, A. Droit, M. Lebel, I. Rudkowska
Journal of Functional Foods, https://doi.org/10.1016/j.jff.2022.105375Decoding Epidermis Reconstruction through Time-course Multi-omics Data Integration
E. Bou Samra, C. Tacheau, M.P. Scott-Boyer, A. Bodein, A. Foucher, K. Abed, V. Segaud, F. Thillou, N. Boyera, N. Misra, A. Droit, O. Perin, N. Cavusoglu
IFSCC Magazine, Volume 25(5), Winner of the Basic Research Award
2022
Overview of methods for characterization and visualization of a protein-protein interaction network in a multi-omics integration context
V. Robin, A. Bodein, M.P. Scott-Boyer, M. Leclercq, O. Perin, A. Droit
Frontiers in Molecular Biosciences, https://doi.org/10.3389/fmolb.2022.962799The interaction of secreted phospholipase A2-IIA with the microbiota alters its lipidome and promotes inflammation
E. Doré, C. Joly-Beauparlant, S. Morozumi, A. Mathieu, T. Lévesque, I. Allaeys, AC. Duchez, N. Cloutier, M. Leclercq, A. Bodein, C. Payré, C. Martin, A. Petit-Paitel, M. H. Gelb, M. Rangachari, M. Murakami, L. Davidovic, N. Flamand, M. Arita, G. Lambeau, A. Droit, E. Boilard
JCI Insight, https://doi.org/10.1172/jci.insight.152638Interpretation of network-based integration from multi-omics longitudinal data
A. Bodein, M.P. Scott-Boyer, O. Perin, K-A. Lê Cao, A. Droit
Nucleic Acids Research, https://doi.org/10.1093/nar/gkab1200timeOmics: an R package for longitudinal multi-omics data integration
A. Bodein, M.P. Scott-Boyer, O. Perin, K-A. Lê Cao, A. Droit
Bioinformatics, https://doi.org/10.1093/bioinformatics/btab664
2021
- Integration strategies of multi-omics data for machine learning analysis
M. Picard, M.P. Scott-Boyer, A. Bodein, O. Perin, A. Droit
Computational and Structural Biotechnology Journal, https://doi.org/10.1016/j.csbj.2021.06.030
2020
- Adipose tissue transcriptome is related to pollutant exposure in polar bear mother-cub pairs from Svalbard, Norway
P. Herst, J. Aars, C. Joly-Beauparlant, A. Bodein, M. Dalvai, D. Gagne, A. Droit, J. Bailey, H. Routti
Environmental Science & Technology, https://doi.org/10.1021/acs.est.0c01920
2019
- A generic multivariate framework for the integration of microbiome longitudinal studies with other data types
A. Bodein, O. Chapleur, A. Droit, K-A. Lê Cao
Frontiers in Genetics, https://doi.org/10.3389/fgene.2019.00963
R Packages
netOmics 2021
A. Bodein , M.P. Scott-Boyer, O. Perin, K-A. Lê Cao, A. Droit
BioConductor (2021) doi.org/10.18129/B9.bioc.netOmicstimeOmics 2019
A. Bodein , O. Chapleur, A. Droit, K-A. Lê Cao BioConductor (2019) doi.org/10.18129/B9.bioc.timeOmics
Talks
- Integration of Microbiome and Multi-Omics Longitudinal Data
A. Bodein , O. Chapleur, A. Droit, K-A. Lê Cao 2019 Presented to : 3 Workshop in Statistical Algorithms Challenges in Microbiome Data Analysis, New-York, USA
Posters
Prediction of Drug-Induced Liver Toxicity through Topological Motif Analysis in Protein Networks May 2025 D. Benyakhlaf, A. Bodein, A. Droit
Presented to : Journées de la Recherche du CHU de Québec, Québec, CanadaAmélioration du repositionnement de médicaments avec l’étiquetage de données négatives grâce aux grands modèles de langage Mar. 2025
M. Picard, M. Leclercq, A. Bodein, M.P. Scott-Boyer, O. Perin, A. Droit
Presented to : Journée de l’Axe Endo-néphrologie, Québec, CanadaTissue-specific network analysis to predict the hepatotoxicity of compounds Aug. 2023
M.P. Scott-Boyer, A. Bodein, R. Grall, B. Ambroise, A. Riu, O. Perin, A. Droit
Presented to : 12th World Congress on Alternatives and Animal Use in the Life Sciences, Niagara Falls, CanadaA framework to integrate multi-omics longitudinal dataset Sept. 2019
M.P. Scott-Boyer, A. Bodein, K-A. Lê Cao, O. Perin, A. Droit
Presented to : EMBO|EMBL - Multiomics to Mechanisms – Challenges in Data Integration, Heidelberg, GermanyIntegration of Microbiome and Multi-Omics Longitudinal Data May 2019
A. Bodein, O. Chapleur, A. Droit, K-A. Lê Cao
Presented to : Journées de la Recherche du CHU de Québec, Québec, CanadaWHORMSS® : Taxonomic and functional exploration from metagenome shotgun sequencing July 2017
Y. Laurent, J. Denonfoux, A. Bodein, S. Ferreira
Presented to : Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Lille, France